Martin Narey, the Director General of the Prison Service, said the theft at Standford Hill was discovered yesterday.
Home Office sources discounted that the stolen papers were the source of a story in a Sunday tabloid about Mr Aitken's pre-Christmas release. One said: "If they had the papers they would not have got the story wrong."
Aitken has been granted leave from Standford Hill prison, a minimum security jail on the Isle of Sheppey, Kent, on 24 December to spend the festive season with his family but is due to return on 30 December.
"He will receive no special treatment. The six days leave at Christmas was assessed in the same way as all other prisoners, and he will be back in jail for 30 December," said a Prison Office spokesman.
The 57-year-old, who served as Chief Secretary to the Treasury under the last Government, will be released on 7 January after serving six-and- a-half months of an 18 month sentence for perjury and perverting the course of justice.